# Calculate H3K4me3 signal on long genes using SAP- adjusted factors (computed in CTCF regions)

11th June 2020

# Summary for H3K4me3
## `Linear regression equations fit to data:` --> general formula: *H3K4me3.signal = (\alpha/ * WCE.signal) + Intercept

- 0h Rep1: H3K4me3.signal = (0.96111 * WCE.signal) + 27.42451 - 1h Rep1: H3K4me3.signal = (0.11971 * WCE.signal) + 6.64561 - 4h Rep1: H3K4me3.signal = (0.44505 * WCE.signal) + 12.22014

- 0h Rep2: H3K4me3.signal = (0.34377 * WCE.signal) + 13.10884 - 1h Rep2: H3K4me3.signal = (0.25230 * WCE.signal) + 10.46680 - 4h Rep2: H3K4me3.signal = (0.21612 * WCE.signal) + 3.01524

#Import libraries needed for data analysis and plotting
suppressPackageStartupMessages({
    library(rtracklayer)
    library(optparse)
    library(GenomicRanges)
    library(gridExtra)  
    library(DESeq2)
    library(umap)
    library(BRGenomics)
    library(tidyverse)
    library(viridis)
    library(ggpointdensity)
});

options(jupyter.plot_mimetypes="image/svg+xml", repr.plot.width=3, repr.plot.height=2);

#1. Import coordinates of maxTSS in K562:
        #Read in enhancers and promtoers maxTSS
            promoters.maxTSS = read.table("/local/storage/data/hg19/k562/copro/promoter.maxTSS.K562.bed", header = T);
            enhancers.maxTSS = read.table("/local/storage/data/hg19/k562/copro/enhancers.maxTSS.K562.bed", header = T);

        #Convert them to GRanges
            promoters.maxTSS = makeGRangesFromDataFrame(promoters.maxTSS);
            enhancers.maxTSS = makeGRangesFromDataFrame(enhancers.maxTSS);

        #Resize them to 4kb: each entries consists of the base-start positions of each maxTSS
            promoters.maxTSS = promoters(promoters.maxTSS, upstream=2000, downstream=2000);
            enhancers.maxTSS = promoters(enhancers.maxTSS, upstream=2000, downstream=2000);


        

(promoters.maxTSS)

GRanges object with 11462 ranges and 0 metadata columns:
          seqnames            ranges strand
             <Rle>         <IRanges>  <Rle>
      [1]     chr6 27858964-27862963      -
      [2]    chr19 47727531-47731530      +
      [3]     chr7 26238367-26242366      -
      [4]     chr6 27112885-27116884      +
      [5]    chr11 65264516-65268515      +
      ...      ...               ...    ...
  [11458]    chr20 62166820-62170819      +
  [11459]    chr21 42790562-42794561      +
  [11460]    chr22 37606696-37610695      +
  [11461]    chr22 45403975-45407974      +
  [11462]     chrX 86770793-86774792      +
  -------
  seqinfo: 23 sequences from an unspecified genome; no seqlengths

all.TSS = append(promoters.maxTSS, enhancers.maxTSS);

all.TSS

GRanges object with 26340 ranges and 0 metadata columns:
          seqnames              ranges strand
             <Rle>           <IRanges>  <Rle>
      [1]     chr6   27858964-27862963      -
      [2]    chr19   47727531-47731530      +
      [3]     chr7   26238367-26242366      -
      [4]     chr6   27112885-27116884      +
      [5]    chr11   65264516-65268515      +
      ...      ...                 ...    ...
  [26336]     chrX 106394425-106398424      +
  [26337]     chrX 129215275-129219274      +
  [26338]     chrX 131136963-131140962      +
  [26339]     chrX 151155950-151159949      +
  [26340]     chrX 152542098-152546097      +
  -------
  seqinfo: 23 sequences from an unspecified genome; no seqlengths

#1. Import gene coordinates in hg19
    genes=read.table("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/gencode.v19.annotation.gtf.gz", header=F, stringsAsFactors=F);
    colnames(genes) = c("chr", "Transcript", "start", "end", "strand", "gene_id", "transcript_id", "gene_type", "gene_name", "TranscriptName");
    genes = genes[genes$Transcript =="transcript",];
    genes = as(genes, "GRanges");

    #Order genes based on their length
    genes = genes[order(width(genes))];
    genes = genes[!duplicated(genes$gene_name)];
    genes = genes[width(genes) > 250];

    genes_resize = promoters(genes, upstream=2000, downstream=2000);


genes_resize

GRanges object with 19438 ranges and 6 metadata columns:
         seqnames              ranges strand |  Transcript            gene_id
            <Rle>           <IRanges>  <Rle> | <character>        <character>
   41040     chr1   26211851-26215850      + |  transcript  ENSG00000229786.1
  398133     chr2 216667705-216671704      - |  transcript  ENSG00000216721.3
  827754     chr6   29943244-29947243      + |  transcript  ENSG00000204625.6
   98756     chr1   73655539-73659538      - |  transcript  ENSG00000251825.1
  114834     chr1 100562795-100566794      + |  transcript  ENSG00000226952.1
     ...      ...                 ...    ... .         ...                ...
  548232     chr3 139652029-139656028      + |  transcript ENSG00000158258.11
  488244     chr3   50710672-50714671      + |  transcript ENSG00000088538.12
  282161     chr2   60325336-60329335      - |  transcript  ENSG00000271955.1
  924687     chr6 163146797-163150796      - |  transcript ENSG00000185345.14
  278270     chr2   51257739-51261738      + |  transcript  ENSG00000231918.1
             transcript_id      gene_type     gene_name    TranscriptName
               <character>    <character>   <character>       <character>
   41040 ENST00000440710.1     pseudogene       SNRPFP2       SNRPFP2-001
  398133 ENST00000454121.1     pseudogene    AC093850.1    AC093850.1-001
  827754 ENST00000463275.1        lincRNA          HCG9          HCG9-002
   98756 ENST00000516016.1       misc_RNA      RN7SKP19      RN7SKP19-201
  114834 ENST00000443135.1     pseudogene   RP4-714D9.4   RP4-714D9.4-001
     ...               ...            ...           ...               ...
  548232 ENST00000511524.1 protein_coding        CLSTN2        CLSTN2-002
  488244 ENST00000266037.9 protein_coding         DOCK3         DOCK3-001
  282161 ENST00000606382.1        lincRNA RP11-444A22.1 RP11-444A22.1-001
  924687 ENST00000366892.1 protein_coding         PARK2         PARK2-002
  278270 ENST00000440698.1        lincRNA    AC007682.1    AC007682.1-001
  -------
  seqinfo: 7 sequences from an unspecified genome; no seqlengths

#1. Import H3K36me3 and WCE BAMs (as Rdata)
    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_0h_br1.Rdata");
    K4me3_0h_br1 = reads;
    rm(reads)

    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_1h_br1.Rdata");
    K4me3_1h_br1 = reads;
    rm(reads)

    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_4h_br1.Rdata");
    K4me3_4h_br1 = reads;
    rm(reads)


    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_0h_br2.Rdata");
    K4me3_0h_br2 = reads;
    rm(reads)

    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_1h_br2.Rdata");
    K4me3_1h_br2 = reads;
    rm(reads)
    
    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/BAM_files/K4me3_bam/mergedMasked_K4me3_4h_br2.Rdata");
    K4me3_4h_br2 = reads;
    rm(reads)


    #WCE
    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_0h_br1_JJO19.Rdata");
    WCE_0h_br1 = reads;
    rm(reads)

    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_1h_br1_JJO19.Rdata");
    WCE_1h_br1 = reads;
    rm(reads)

    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_4h_br1_JJO19.Rdata");
    WCE_4h_br1 = reads;
    rm(reads)


    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_0h_br2_JJO19.Rdata");
    WCE_0h_br2 = reads;
    rm(reads)

    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_1h_br2_JJO19.Rdata");
    WCE_1h_br2 = reads;
    rm(reads)
    
    load("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/WCE_mergedBAMs_JuneJulyOct2019/BAM_files/WCE_4h_br2_JJO19.Rdata");
    WCE_4h_br2 = reads;
    rm(reads)

Count.reads.InBins = function(mark.BAM, regions, spike = 1, binsize = 1, field = "score"){
    
    #Resize each read from BAM to 1bp (center position of each read)
    mark.BAM.res = resize(mark.BAM, width = 1, fix = "center");
    #Compute coverage
    mark.BAM.res = GRanges(coverage(mark.BAM.res, weight="count"));
    mark.BAM.res = makeGRangesBRG(mark.BAM.res[mark.BAM.res$score > 0]);

    #Count DHS signal within each CTCF peak
    mark.BAM.score = getCountsByPositions(mark.BAM.res, regions, binsize = binsize, field="score");
    
    return(mark.BAM.score/spike)
}

#4. Experimental H3K36me3 signal in regions of interest
    K4me3_0h_br1.perBin     = Count.reads.InBins(K4me3_0h_br1, all.TSS, spike = 1, binsize = 100, field = "score");
    K4me3_1h_br1.perBin     = Count.reads.InBins(K4me3_1h_br1, all.TSS, spike = 1, binsize = 100, field = "score");
    K4me3_4h_br1.perBin     = Count.reads.InBins(K4me3_4h_br1, all.TSS, spike = 1, binsize = 100, field = "score");

    K4me3_0h_br2.perBin     = Count.reads.InBins(K4me3_0h_br2, all.TSS, spike = 1, binsize = 100, field = "score");
    K4me3_1h_br2.perBin     = Count.reads.InBins(K4me3_1h_br2, all.TSS, spike = 1, binsize = 100, field = "score");
    K4me3_4h_br2.perBin     = Count.reads.InBins(K4me3_4h_br2, all.TSS, spike = 1, binsize = 100, field = "score");

#5. WCE reads in regions of interest

    WCE.K27ac_0h_br1.perBin = Count.reads.InBins(WCE_0h_br1,    all.TSS, spike = 1,  binsize = 100, field = "score");
    WCE.K27ac_1h_br1.perBin = Count.reads.InBins(WCE_1h_br1,    all.TSS, spike = 1,  binsize = 100, field = "score");
    WCE.K27ac_4h_br1.perBin = Count.reads.InBins(WCE_4h_br1,    all.TSS, spike = 1,  binsize = 100, field = "score");

    WCE.K27ac_0h_br2.perBin = Count.reads.InBins(WCE_0h_br2,    all.TSS, spike = 1,  binsize = 100, field = "score");
    WCE.K27ac_1h_br2.perBin = Count.reads.InBins(WCE_1h_br2,    all.TSS, spike = 1,  binsize = 100, field = "score");
    WCE.K27ac_4h_br2.perBin = Count.reads.InBins(WCE_4h_br2,    all.TSS, spike = 1,  binsize = 100, field = "score");

#6. Calculate theotic value from the linear regressions and the WCE reads per Bin

    K4me3_0h_br1.theoretic.perBin = (0.96111 * WCE.K27ac_0h_br1.perBin) + 27.42451;
    K4me3_1h_br1.theoretic.perBin = (0.11971 * WCE.K27ac_1h_br1.perBin) + 6.64561;
    K4me3_4h_br1.theoretic.perBin = (0.44505 * WCE.K27ac_4h_br1.perBin) + 12.22014;

    K4me3_0h_br2.theoretic.perBin = (0.34377 * WCE.K27ac_0h_br2.perBin) + 13.10884;
    K4me3_1h_br2.theoretic.perBin = (0.25230 * WCE.K27ac_1h_br2.perBin) + 10.46680;
    K4me3_4h_br2.theoretic.perBin = (0.21612 * WCE.K27ac_4h_br2.perBin) + 3.01524;

#7. Calculate the residuals
    res_0h_br1 = K4me3_0h_br1.perBin - K4me3_0h_br1.theoretic.perBin;
    res_1h_br1 = K4me3_1h_br1.perBin - K4me3_1h_br1.theoretic.perBin;
    res_4h_br1 = K4me3_4h_br1.perBin - K4me3_4h_br1.theoretic.perBin;

    res_0h_br2 = K4me3_0h_br2.perBin - K4me3_0h_br2.theoretic.perBin;
    res_1h_br2 = K4me3_1h_br2.perBin - K4me3_1h_br2.theoretic.perBin;
    res_4h_br2 = K4me3_4h_br2.perBin - K4me3_4h_br2.theoretic.perBin;

#8. Replace all residuals < 0 with 0
    res_0h_br1[res_0h_br1 < 0] = 0;
    res_1h_br1[res_1h_br1 < 0] = 0;
    res_4h_br1[res_4h_br1 < 0] = 0;

    res_0h_br2[res_0h_br2 < 0] = 0;
    res_1h_br2[res_1h_br2 < 0] = 0;
    res_4h_br2[res_4h_br2 < 0] = 0;

#9. Keep only the entries were both replicates have reads
    badgenes_0h = which(rowSums(res_0h_br1)<1 | rowSums(res_0h_br2)<1 | rowSums(res_1h_br1)<1 | rowSums(res_1h_br2)<1 | rowSums(res_4h_br1)<1 | rowSums(res_4h_br2)<1);
    filtered_0h_br1 = res_0h_br1[-badgenes_0h,];
    filtered_0h_br2 = res_0h_br2[-badgenes_0h,];
    
    #1h
    filtered_1h_br1 = res_1h_br1[-badgenes_0h,];
    filtered_1h_br2 = res_1h_br2[-badgenes_0h,];

    #4h
    filtered_4h_br1 = res_4h_br1[-badgenes_0h,];
    filtered_4h_br2 = res_4h_br2[-badgenes_0h,];

length(filtered_0h_br1)

478200

#9. Subsample residual matrices and plot metaplots
    res_0h_br1.subs = metaSubsampleMatrix(filtered_0h_br1  /2530);
    res_1h_br1.subs = metaSubsampleMatrix(filtered_1h_br1  /3048);
    res_4h_br1.subs = metaSubsampleMatrix(filtered_4h_br1  /4108);

    res_0h_br2.subs = metaSubsampleMatrix(filtered_0h_br2  /346 * 0.267234624149712);
    res_1h_br2.subs = metaSubsampleMatrix(filtered_1h_br2  /1724 * 0.267234624149712);
    res_4h_br2.subs = metaSubsampleMatrix(filtered_4h_br2  /1782 * 0.267234624149712);

#10. Give miningful names to each dataset --> thse names will be used as labels for the plot 
    res_0h_br1.subs$sample.name = "0h Rep1";
    res_1h_br1.subs$sample.name = "1h Rep1";
    res_4h_br1.subs$sample.name = "4h Rep1";

    res_0h_br2.subs$sample.name = "0h Rep2";
    res_1h_br2.subs$sample.name = "1h Rep2";
    res_4h_br2.subs$sample.name = "4h Rep2";

theme_set(
   theme_classic() +
        theme(
            panel.border = element_blank(),  
            # Remove panel background
            panel.background = element_blank(),
            legend.background = element_blank(),
            # Add axis line
            axis.line = element_line(colour = "black", size=0.5),
            panel.grid.major = element_line(colour = "white"),
            axis.text.x = element_text( color="black", size=14),
            axis.text.y = element_text( color="black", size=16),
            axis.title.x = element_text(color="black", size=14),
            axis.title.y = element_text(color="black", size=16)
            )
);

####All gencode annotated genes


#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles 


# ----> Promoters

plot_BR1.RPM = rbind(res_0h_br1.subs, res_1h_br1.subs, res_4h_br1.subs);

        ggplot(plot_BR1.RPM, aes(x=x, y=mean, color=sample.name)) +
        geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
        geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +        
        scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
        labs(
            #title = "\n H3K4me3 promoters - Replicate 1 \n ",
            x = "Distance from TSS [kb]",
            y = "Normalized \n signal"
        ) 



plot_BR2.RPM = rbind(res_0h_br2.subs, res_1h_br2.subs, res_4h_br2.subs);

        ggplot(plot_BR2.RPM, aes(x=x, y=mean, color=sample.name)) +
        geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
        geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +        
        scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
        labs(
            #title = "\n H3K4me3 promoters - Replicate 2 \n ",
            x = "Distance from TSS [kb]",
            y = "Normalized \n signal"
        )

####All gencode annotated genes


#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles 


# ----> Promoters

plot_BR1.RPM = rbind(res_0h_br1.subs, res_1h_br1.subs, res_4h_br1.subs);

        ggplot(plot_BR1.RPM, aes(x=x, y=mean, color=sample.name)) +
        geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
        geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +        
        scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
        labs(
            #title = "\n H3K4me3 promoters - Replicate 1 \n ",
            x = "Distance from TSS [kb]",
            y = "Normalized \n signal"
        ) 



plot_BR2.RPM = rbind(res_0h_br2.subs, res_1h_br2.subs, res_4h_br2.subs);

        ggplot(plot_BR2.RPM, aes(x=x, y=mean, color=sample.name)) +
        geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
        geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +        
        scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
        labs(
            #title = "\n H3K4me3 promoters - Replicate 2 \n ",
            x = "Distance from TSS [kb]",
            y = "Normalized \n signal"
        )

#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles 


# ----> Promoters

plot_BR1.RPM = rbind(res_0h_br1.subs, res_1h_br1.subs, res_4h_br1.subs);

        ggplot(plot_BR1.RPM, aes(x=x, y=mean, color=sample.name)) +
        geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
        geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +        
        scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
        labs(
            #title = "\n H3K4me3 promoters - Replicate 1 \n ",
            x = "Distance from TSS [kb]",
            y = "Normalized \n signal"
        ) 



plot_BR2.RPM = rbind(res_0h_br2.subs, res_1h_br2.subs, res_4h_br2.subs);

        ggplot(plot_BR2.RPM, aes(x=x, y=mean, color=sample.name)) +
        geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
        geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_continuous(labels = c(0, 10, 20), breaks=c(0.00, 0.01, 0.02)) +        
        scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
        labs(
            #title = "\n H3K4me3 promoters - Replicate 2 \n ",
            x = "Distance from TSS [kb]",
            y = "Normalized \n signal"
        )

sum(res_0h_br1.subs$mean)/sum(res_0h_br2.subs$mean)

0.267234624149712

# Compare replicates

Correlations between repliates will be determined by coputing a K-S test and by making scatter plots using data from the same time points in both biological replicates.

Good correlation between replicates will be indicated by a D ~ 0 (in the K-S test), and by data points in scatter plot aproaching the x=y diagonal.

A violin plot with very similar, if not the same, mean values in both replicates can be an alternative for the scatter plot.

Promoters

#Remove top and bottom 2.5% of data for K-S tests
    #rSums_0h_br1 = rowSums(filtered_0h_br1)[round(0.025*length(rowSums(filtered_0h_br1))):round(0.975* length(rowSums(filtered_0h_br1)))]/3002;
    #rSums_1h_br1 = rowSums(filtered_1h_br1)[round(0.025*length(rowSums(filtered_1h_br1))):round(0.975* length(rowSums(filtered_1h_br1)))]/9218;
    #rSums_4h_br1 = rowSums(filtered_4h_br1)[round(0.025*length(rowSums(filtered_4h_br1))):round(0.975* length(rowSums(filtered_4h_br1)))]/8084;


    #Rep 2:
    #rSums_0h_br2 = rowSums(filtered_0h_br2)[round(0.025*length(rowSums(filtered_0h_br2))):round(0.975* length(rowSums(filtered_0h_br2)))]/1042 * 0.673771984137532;
    #rSums_1h_br2 = rowSums(filtered_1h_br2)[round(0.025*length(rowSums(filtered_1h_br2))):round(0.975* length(rowSums(filtered_1h_br2)))]/7368 * 0.673771984137532;
    #rSums_4h_br2 = rowSums(filtered_4h_br2)[round(0.025*length(rowSums(filtered_4h_br2))):round(0.975* length(rowSums(filtered_4h_br2)))]/7984 * 0.673771984137532;


rSums_0h_br1 = rowSums(filtered_0h_br1)/2530;
rSums_1h_br1 = rowSums(filtered_1h_br1)/3048;
rSums_4h_br1 = rowSums(filtered_4h_br1)/4108;


rSums_0h_br2 = rowSums(filtered_0h_br2)/346 * 0.267234624149712;
rSums_1h_br2 = rowSums(filtered_1h_br2)/1724 * 0.267234624149712;
rSums_4h_br2 = rowSums(filtered_4h_br2)/1782 * 0.267234624149712;

#Left merge the 2 peaks (knowing that they have the same peak.name column, in the same order)
            # 0h
                mark_0h = cbind((rSums_0h_br1), (rSums_0h_br2));
                colnames(mark_0h) = c("Rep1", "Rep2");
            # 1h
                mark_1h = cbind((rSums_1h_br1), (rSums_1h_br2));
                colnames(mark_1h) = c("Rep1", "Rep2");
            # 4h
                mark_4h = cbind((rSums_4h_br1), (rSums_4h_br2));
                colnames(mark_4h) = c("Rep1", "Rep2");

### VII. Plot and correlate 0h datasets

#For correlations can also use:
cor.test(mark_0h[, "Rep1"], mark_0h[, "Rep2"], method = "pearson");
cor.test(mark_0h[, "Rep1"], mark_0h[, "Rep2"], method = "spearman");

	Pearson's product-moment correlation

data:  mark_0h[, "Rep1"] and mark_0h[, "Rep2"]
t = 448.13, df = 9250, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.9768202 0.9786155
sample estimates:
      cor 
0.9777357 

Warning message in cor.test.default(mark_0h[, "Rep1"], mark_0h[, "Rep2"], method = "spearman"):
"Cannot compute exact p-value with ties"

	Spearman's rank correlation rho

data:  mark_0h[, "Rep1"] and mark_0h[, "Rep2"]
S = 4211065336, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.9680966 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(mark_0h), mapping=aes(Rep2, Rep1)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n H3K4me3 - 4kb around promoter TSSs \n P = 0.9787136, S = 0.9707956 \n",
        x = "Rep II 0h",
        y = "Rep I 0h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

### VII. Plot and correlate 0h datasets

#For correlations can also use:
cor.test(mark_1h[, "Rep1"], mark_1h[, "Rep2"], method = "pearson");
cor.test(mark_1h[, "Rep1"], mark_1h[, "Rep2"], method = "spearman");

	Pearson's product-moment correlation

data:  mark_1h[, "Rep1"] and mark_1h[, "Rep2"]
t = 183.95, df = 9839, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.8756541 0.8845588
sample estimates:
      cor 
0.8801839 

	Spearman's rank correlation rho

data:  mark_1h[, "Rep1"] and mark_1h[, "Rep2"]
S = 2.0899e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.8684296 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(mark_1h), mapping=aes(Rep2, Rep1)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n H3K4me3 - 4kb around promoter TSSs \n P = 0.8801839, S = 0.8684298 \n",
        x = "Rep II 1h",
        y = "Rep I 1h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

### VII. Plot and correlate 0h datasets

#For correlations can also use:
cor.test(mark_4h[, "Rep1"], mark_4h[, "Rep2"], method = "pearson");
cor.test(mark_4h[, "Rep1"], mark_4h[, "Rep2"], method = "spearman");

	Pearson's product-moment correlation

data:  mark_4h[, "Rep1"] and mark_4h[, "Rep2"]
t = 170.59, df = 9839, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.8594043 0.8693915
sample estimates:
      cor 
0.8644832 

	Spearman's rank correlation rho

data:  mark_4h[, "Rep1"] and mark_4h[, "Rep2"]
S = 2.3863e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.8497667 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(mark_4h), mapping=aes(Rep2, Rep1)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n H3K4me3 - 4kb around promoter TSSs \n P = 0.8644832, S = 0.8497667 \n",
        x = "Rep II 4h",
        y = "Rep I 4h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

Computing K-S test between replicates

ks.test(mark_0h[, "Rep1"], mark_0h[, "Rep2"]);

Warning message in ks.test(mark_0h[, "Rep1"], mark_0h[, "Rep2"]):
"p-value will be approximate in the presence of ties"

	Two-sample Kolmogorov-Smirnov test

data:  mark_0h[, "Rep1"] and mark_0h[, "Rep2"]
D = 0.035452, p-value = 1.782e-05
alternative hypothesis: two-sided

#Plot the samples together
x = append(mark_0h[, "Rep1"], mark_0h[, "Rep2"]);
  lab = gl(2, length(mark_0h[, "Rep1"]), labels = c("0h_br1", "0h_br2"));


ggplot(as.data.frame(cbind(x, lab)), aes(x=as.numeric(x), group = as.numeric(lab), col=lab)) + stat_ecdf(geom = "point") + 
    scale_x_log10() + 
    labs(
            title = "\n K-S test: 0h Rep1 vs 0h Rep2 \n D = 0.035057 \n",
            x = " Log Residual H3K4me3 1h"
        ) +
        theme_classic() +
        theme(
            #panel.border = element_blank(),  
            # Remove panel background
            panel.background = element_blank(),
            legend.background = element_blank(),
            # Add axis line
            axis.line = element_line(colour = "black", size=1),
            panel.grid.major = element_line(colour = "white"),
            plot.title = element_text(color="black", size=28, face="bold", hjust = 0.5),
            axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
            axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
            axis.title.x = element_text(color="black", size=24, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
            axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
        )

ks.test(mark_1h[, "Rep1"], mark_1h[, "Rep2"]);

	Two-sample Kolmogorov-Smirnov test

data:  mark_1h[, "Rep1"] and mark_1h[, "Rep2"]
D = 0.42191, p-value < 2.2e-16
alternative hypothesis: two-sided

#Plot the samples together
x = append(mark_1h[, "Rep1"], mark_1h[, "Rep2"]);
  lab = gl(2, length(mark_1h[, "Rep1"]), labels = c("1h_br1", "1h_br2"));


ggplot(as.data.frame(cbind(x, lab)), aes(x=as.numeric(x), group = as.numeric(lab), col=lab)) + stat_ecdf(geom = "point") + 
    scale_x_log10() + 
    labs(
            title = "\n K-S test: 1h Rep1 vs 0h Rep2 \n D = 0.42191 \n",
            x = " Log Residual H3K4me3 1h"
        ) +
        theme_classic() +
        theme(
            #panel.border = element_blank(),  
            # Remove panel background
            panel.background = element_blank(),
            legend.background = element_blank(),
            # Add axis line
            axis.line = element_line(colour = "black", size=1),
            panel.grid.major = element_line(colour = "white"),
            plot.title = element_text(color="black", size=28, face="bold", hjust = 0.5),
            axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
            axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
            axis.title.x = element_text(color="black", size=24, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
            axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
        )

ks.test(mark_4h[, "Rep1"], mark_4h[, "Rep2"]);

	Two-sample Kolmogorov-Smirnov test

data:  mark_4h[, "Rep1"] and mark_4h[, "Rep2"]
D = 0.48765, p-value < 2.2e-16
alternative hypothesis: two-sided

#Plot the samples together
x = append(mark_4h[, "Rep1"], mark_4h[, "Rep2"]);
  lab = gl(2, length(mark_4h[, "Rep1"]), labels = c("4h_br1", "4h_br2"));


ggplot(as.data.frame(cbind(x, lab)), aes(x=as.numeric(x), group = as.numeric(lab), col=lab)) + stat_ecdf(geom = "point") + 
    scale_x_log10() + 
    labs(
            title = "\n K-S test: 4h Rep1 vs 0h Rep2 \n D = 0.48765 \n",
            x = " Log Residual H3K4me3 4h"
        ) +
        theme_classic() +
        theme(
            #panel.border = element_blank(),  
            # Remove panel background
            panel.background = element_blank(),
            legend.background = element_blank(),
            # Add axis line
            axis.line = element_line(colour = "black", size=1),
            panel.grid.major = element_line(colour = "white"),
            plot.title = element_text(color="black", size=28, face="bold", hjust = 0.5),
            axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
            axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
            axis.title.x = element_text(color="black", size=24, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
            axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
        )

Draw Violin plots to show the distribution of normalized H3K4me3 signal at promoters

library(tidyverse)
mark_violin = tibble(
    R1_0h=mark_0h[, "Rep1"],
    R2_0h=mark_0h[, "Rep2"],
    R1_1h=mark_1h[, "Rep1"],
    R2_1h=mark_1h[, "Rep2"],
    R1_4h=mark_4h[, "Rep1"],
    R2_4h=mark_4h[, "Rep2"],
    ID = 1:length(R1_0h)
) %>%
pivot_longer( R1_0h:R2_4h, names_to = "Sample", values_to = "Signal" ) %>%
#substr = select from column "Sample" at start=2, end=2
mutate( Rep=substr(Sample, 2, 2), time=substr(Sample, 4, 5) );

# ---> Promoters

ggplot(mark_violin, aes(x=paste0(time, Rep), y=as.numeric(Signal), col=time)) +  
        geom_violin(draw_quantiles = c(0.25, 0.5, 0.75), alpha=0.5, lwd=0.5, show.legend = F ) +
        scale_y_log10(labels = c(0.0001, 0.01, 1), breaks=c(1e-04, 1e-02, 1e+00)) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        labs(
            x = "",
            y = "Log normalized"
        ) +
        scale_x_discrete()

Warning message:
"Transformation introduced infinite values in continuous y-axis"
Warning message:
"Removed 402 rows containing non-finite values (stat_ydensity)."

ggplot(mark_violin, aes(x=paste0(time, Rep), y=as.numeric(Signal), col=time)) +  
        geom_violin(draw_quantiles = c(0.25, 0.5, 0.75), alpha=0.5, lwd=0.5, show.legend = F) +
        scale_y_log10(labels = c(0.0001, 0.01, 1), breaks=c(1e-04, 1e-02, 1e+00)) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_log10() +
        labs(
            x = "",
            y = "Relative signal"
        ) +
        scale_x_discrete()

Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.

XII. Draw PCA for normalized H3K4me3 signal within peaks

#1. Merge all signals per peaks into one signle matrix
    mark_PCA = cbind(as.numeric(mark_0h[, "Rep1"]), as.numeric(mark_1h[, "Rep1"]),
                     as.numeric(mark_4h[, "Rep1"]), as.numeric(mark_0h[, "Rep2"]),
                     as.numeric(mark_1h[, "Rep2"]), as.numeric(mark_4h[, "Rep2"]));
    colnames(mark_PCA) = c("H3K4me3 0h BR1", "H3K4me3 1h BR1", "H3K4me3 4h BR1", "H3K27H3K4me3c 0h BR2", "H3K4me3 1h BR2", "H3K4me3 4h BR2");

    #If any, replace all NAs with 0
    mark_PCA[is.na(mark_PCA)] = 0;

    head(mark_PCA)

A matrix: 6 × 6 of type dbl

H3K4me3 0h BR1	H3K4me3 1h BR1	H3K4me3 4h BR1	H3K27H3K4me3c 0h BR2	H3K4me3 1h BR2	H3K4me3 4h BR2
0.8105001	0.08513178	0.15229185	0.6295785	0.08982861	0.1633068
0.5552439	0.06959867	0.10917628	0.4821538	0.04467459	0.1135402
0.5368228	0.07509226	0.08996878	0.3989542	0.07055816	0.1213926
0.3906044	0.06263347	0.09843864	0.3276587	0.03615007	0.0834512
0.3628903	0.03356353	0.07138911	0.3400055	0.04185720	0.1108769
0.6122549	0.08207975	0.09343375	0.4286424	0.07611265	0.1291515

#Make PCA:
options(jupyter.plot_mimetypes="image/svg+xml", repr.plot.width=7, repr.plot.height=8);

cols <-  rep(1:2, each=3);
pch <- c(rep(c(1:3),2));
legend <- colnames(mark_PCA);

pc.cr <- princomp(mark_PCA, cor = TRUE)
pairs(pc.cr$loadings[, 1:5], col=cols, pch=pch)
#legend("bottomleft", pch=c(1:3), legend=colnames(K27ac_PCA))

summary(pc.cr)

Importance of components:
                          Comp.1     Comp.2      Comp.3      Comp.4      Comp.5
Standard deviation     2.3669389 0.51225802 0.235219719 0.208576470 0.157429772
Proportion of Variance 0.9337333 0.04373471 0.009221386 0.007250691 0.004130689
Cumulative Proportion  0.9337333 0.97746798 0.986689361 0.993940052 0.998070741
                            Comp.6
Standard deviation     0.107589761
Proportion of Variance 0.001929259
Cumulative Proportion  1.000000000

# Average the 2 replicates - instead of merging them

#1. Average normalized replicates
    filtered_0h = ((res_0h_br1  /2530) + (res_0h_br2  /346))/2;
    filtered_1h = ((res_1h_br1  /3048) + (res_1h_br2  /1724))/2;
    filtered_4h = ((res_4h_br1  /4108) + (res_4h_br2  /1782))/2;

#write.table(rowSums(filtered_0h), "./K4me3.allTSS.4kb_0h_ReadyForPlotting.bed", quote=F, sep="\t", row.names=F, col.names=F);
#write.table(rowSums(filtered_1h), "./K4me3.allTSS.4kb_1h_ReadyForPlotting.bed", quote=F, sep="\t", row.names=F, col.names=F);
#write.table(rowSums(filtered_4h), "./K4me3.allTSS.4kb_4h_ReadyForPlotting.bed", quote=F, sep="\t", row.names=F, col.names=F);

#9. Subsample residual matrices and plot metaplots
    res_0h.subs = metaSubsampleMatrix(filtered_0h);
    res_1h.subs = metaSubsampleMatrix(filtered_1h);
    res_4h.subs = metaSubsampleMatrix(filtered_4h);

#10. Give miningful names to each dataset --> thse names will be used as labels for the plot 
    res_0h.subs$sample.name = "0h ";
    res_1h.subs$sample.name = "1h ";
    res_4h.subs$sample.name = "4h ";

theme_set(
   theme_classic() +
        theme(
            panel.border = element_blank(),  
            # Remove panel background
            panel.background = element_blank(),
            legend.background = element_blank(),
            # Add axis line
            axis.line = element_line(colour = "black", size=0.5),
            panel.grid.major = element_line(colour = "white"),
            axis.text.x = element_text( color="black", size=14),
            axis.text.y = element_text( color="black", size=16),
            axis.title.x = element_text(color="black", size=14),
            axis.title.y = element_text(color="black", size=16)
            )
);

#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles ---> RPM norm data

# --> Enhancers

options(jupyter.plot_mimetypes="image/svg+xml", repr.plot.width=3, repr.plot.height=2);

plot.merged = rbind(res_0h.subs, res_1h.subs, res_4h.subs);

        ggplot(plot.merged, aes(x=x, y=mean, color=sample.name)) +
        geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
        geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
        #scale_colour_manual(values = c("#005ab3", "#ff8da1", "#ff6500")) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_continuous(labels = c(0, 2, 4), breaks=c(0.00, 0.02, 0.04)) +
        scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
        labs(
            x = " Distance to TSS [kb]",
            y =  "Normalized \n signal "
        )

Draw Violin plots to show the distribution of normalized H3K4me3 signal at promoters

mark_violin = tibble(
    R1_0h=rowSums(filtered_0h),
    R1_1h=rowSums(filtered_1h),
    R1_4h=rowSums(filtered_4h),

    ID = 1:length(R1_0h)
) %>%
pivot_longer( R1_0h:R1_4h, names_to = "Sample", values_to = "Signal" ) %>%
#substr = select from column "Sample" at start=2, end=2
mutate( Rep=substr(Sample, 2, 2), time=substr(Sample, 4, 5) );

ggplot(mark_violin, aes(x=paste0(time, " "), y=as.numeric(Signal), col=time)) +  
        geom_violin(draw_quantiles = c(0.25, 0.5, 0.75), alpha=0.5, lwd=0.5, show.legend = F ) +
        scale_y_log10(labels = c(0.0001, 0.01, 1), breaks=c(1e-04, 1e-02, 1e+00)) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        labs(
            x = "",
            y = "\n Log normalized \n "
        ) +
        scale_x_discrete()

Warning message:
"Transformation introduced infinite values in continuous y-axis"
Warning message:
"Removed 2 rows containing non-finite values (stat_ydensity)."

#Wilcox test
wilcox.test(filtered_0h, filtered_1h, mu = 0, paired=F, alternative = "two.sided", conf.int=T, conf.level = 0.95, exact=T)
wilcox.test(filtered_0h, filtered_4h, mu = 0, paired=F, alternative = "two.sided", conf.int=T, conf.level = 0.95, exact=T)

Warning message in wilcox.test.default(filtered_0h, filtered_1h, mu = 0, paired = F, :
"cannot compute exact p-value with ties"
Warning message in wilcox.test.default(filtered_0h, filtered_1h, mu = 0, paired = F, :
"cannot compute exact confidence intervals with ties"

	Wilcoxon rank sum test with continuity correction

data:  filtered_0h and filtered_1h
W = 8.6175e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
 3.852630e-05 3.044874e-05
sample estimates:
difference in location 
          4.329485e-05 

Warning message in wilcox.test.default(filtered_0h, filtered_4h, mu = 0, paired = F, :
"cannot compute exact p-value with ties"
Warning message in wilcox.test.default(filtered_0h, filtered_4h, mu = 0, paired = F, :
"cannot compute exact confidence intervals with ties"

	Wilcoxon rank sum test with continuity correction

data:  filtered_0h and filtered_4h
W = 7.3154e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
 -1.839428e-05 -4.791938e-05
sample estimates:
difference in location 
         -6.576012e-05 

wilcox.test(filtered_1h, filtered_4h, mu = 0, paired=F, alternative = "two.sided", exact=T)

Warning message in wilcox.test.default(filtered_1h, filtered_4h, mu = 0, paired = F, :
"cannot compute exact p-value with ties"

	Wilcoxon rank sum test with continuity correction

data:  filtered_1h and filtered_4h
W = 6.0277e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0

Draw Violin plots to show the distribution of normalized H3K4me3 signal at enhancers

mark_violin = tibble(
    R1_0h=rowSums(filtered_0h),
    R1_1h=rowSums(filtered_1h),
    R1_4h=rowSums(filtered_4h),

    ID = 1:length(R1_0h)
) %>%
pivot_longer( R1_0h:R1_4h, names_to = "Sample", values_to = "Signal" ) %>%
#substr = select from column "Sample" at start=2, end=2
mutate( Rep=substr(Sample, 2, 2), time=substr(Sample, 4, 5) );

ggplot(mark_violin, aes(x=paste0(time, " "), y=as.numeric(Signal), col=time)) +  
        geom_violin(draw_quantiles = c(0.25, 0.5, 0.75), alpha=0.5, lwd=0.5, show.legend = F ) +
        scale_y_log10(labels = c(0.0001, 0.01, 1), breaks=c(1e-04, 1e-02, 1e+00)) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        labs(
            x = "",
            y = "\n Relative signal "
        ) +
        scale_x_discrete()

Warning message:
"Transformation introduced infinite values in continuous y-axis"
Warning message:
"Removed 2 rows containing non-finite values (stat_ydensity)."

#Wilcox test
wilcox.test(filtered_0h, filtered_1h, mu = 0, paired=F, alternative = "two.sided", conf.int=T, conf.level = 0.95, exact=T)
wilcox.test(filtered_0h, filtered_4h, mu = 0, paired=F, alternative = "two.sided", conf.int=T, conf.level = 0.95, exact=T)

Warning message in wilcox.test.default(filtered_0h, filtered_1h, mu = 0, paired = F, :
"cannot compute exact p-value with ties"
Warning message in wilcox.test.default(filtered_0h, filtered_1h, mu = 0, paired = F, :
"cannot compute exact confidence intervals with ties"

	Wilcoxon rank sum test with continuity correction

data:  filtered_0h and filtered_1h
W = 8.6175e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
 3.852630e-05 3.044874e-05
sample estimates:
difference in location 
          4.329485e-05 

Warning message in wilcox.test.default(filtered_0h, filtered_4h, mu = 0, paired = F, :
"cannot compute exact p-value with ties"
Warning message in wilcox.test.default(filtered_0h, filtered_4h, mu = 0, paired = F, :
"cannot compute exact confidence intervals with ties"

	Wilcoxon rank sum test with continuity correction

data:  filtered_0h and filtered_4h
W = 7.3154e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
 -1.839428e-05 -4.791938e-05
sample estimates:
difference in location 
         -6.576012e-05 

Plot H3K27ac at promoters that lost H3K4me1

</center>

#Import coordinates of promoters that lost H3K4me1
    K4me1.loss = read.table("../K4me1/GenePromoters_ThatLose.K4me1.bed");
    colnames(K4me1.loss) = c("chr", "start", "end", "width", "log2FC_10");

    K4me1.loss = makeGRangesFromDataFrame(K4me1.loss);
    K4me1.loss = resize(K4me1.loss, width = 4000, fix = "start");
    #K4me1.loss = promoters(K4me1.loss, upstream=0, downstream=2000);

K4me1.loss

GRanges object with 430 ranges and 0 metadata columns:
        seqnames              ranges strand
           <Rle>           <IRanges>  <Rle>
    [1] \303chr2 122286456-122290455      *
    [2]     chr1   25553946-25557945      *
    [3]    chr19   49373678-49377677      *
    [4]     chr1 109640815-109644814      *
    [5]     chr9 127983623-127987622      *
    ...      ...                 ...    ...
  [426]    chr15   40381114-40385113      *
  [427]    chr15   43510973-43514972      *
  [428]     chr3   39214085-39218084      *
  [429]    chr12   52279888-52283887      *
  [430]    chr16     2519481-2523480      *
  -------
  seqinfo: 23 sequences from an unspecified genome; no seqlengths

#4. Experimental H3K36me3 signal in regions of interest
    K4me3_0h_br1.perBin     = Count.reads.InBins(K4me3_0h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");
    K4me3_1h_br1.perBin     = Count.reads.InBins(K4me3_1h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");
    K4me3_4h_br1.perBin     = Count.reads.InBins(K4me3_4h_br1, K4me1.loss, spike = 1, binsize = 100, field = "score");

    K4me3_0h_br2.perBin     = Count.reads.InBins(K4me3_0h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");
    K4me3_1h_br2.perBin     = Count.reads.InBins(K4me3_1h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");
    K4me3_4h_br2.perBin     = Count.reads.InBins(K4me3_4h_br2, K4me1.loss, spike = 1, binsize = 100, field = "score");

Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, 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HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, 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HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaffold_455, HiC_scaff"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_scaffold_447, HiC_scaffold_448, HiC_scaffold_449, HiC_scaffold_450, HiC_scaffold_451, HiC_scaffold_452, HiC_scaffold_453, HiC_scaffold_454, HiC_scaff"

#5. WCE reads in regions of interest

    WCE.K27ac_0h_br1.perBin = Count.reads.InBins(WCE_0h_br1,    K4me1.loss, spike = 1,  binsize = 100, field = "score");
    WCE.K27ac_1h_br1.perBin = Count.reads.InBins(WCE_1h_br1,    K4me1.loss, spike = 1,  binsize = 100, field = "score");
    WCE.K27ac_4h_br1.perBin = Count.reads.InBins(WCE_4h_br1,    K4me1.loss, spike = 1,  binsize = 100, field = "score");

    WCE.K27ac_0h_br2.perBin = Count.reads.InBins(WCE_0h_br2,    K4me1.loss, spike = 1,  binsize = 100, field = "score");
    WCE.K27ac_1h_br2.perBin = Count.reads.InBins(WCE_1h_br2,    K4me1.loss, spike = 1,  binsize = 100, field = "score");
    WCE.K27ac_4h_br2.perBin = Count.reads.InBins(WCE_4h_br2,    K4me1.loss, spike = 1,  binsize = 100, field = "score");

Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_scaffold_446, HiC_s"
Warning message in .Seqinfo.mergexy(x, y):
"Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': <c3>chr2
  - in 'y': chrX, chrY, rRNA, dm3chr2L, dm3chr2LHet, dm3chr2R, dm3chr2RHet, dm3chr3L, dm3chr3LHet, dm3chr3R, dm3chr3RHet, dm3chr4, dm3chrM, dm3chrUextra, dm3chrU, dm3chrX, dm3chrXHet, dm3chrYHet, HiC_scaffold_1, HiC_scaffold_2, HiC_scaffold_3, HiC_scaffold_4, HiC_scaffold_5, HiC_scaffold_6, HiC_scaffold_7, HiC_scaffold_8, HiC_scaffold_9, HiC_scaffold_10, HiC_scaffold_11, HiC_scaffold_12, HiC_scaffold_13, HiC_scaffold_14, HiC_scaffold_15, HiC_scaffold_16, HiC_scaffold_17, HiC_scaffold_18, HiC_scaffold_19, HiC_scaffold_20, HiC_scaffold_21, HiC_scaffold_22, HiC_scaffold_23, HiC_scaffold_24, HiC_scaffold_25, HiC_scaffold_26, HiC_scaffold_27, HiC_scaffold_28, HiC_scaffold_29, HiC_scaffold_30, HiC_scaffold_31, HiC_scaffold_32, HiC_scaffold_33, HiC_scaffold_34, HiC_scaffold_35, HiC_scaffold_36, HiC_scaffold_37, HiC_scaffold_38, HiC_scaffold_39, HiC_scaffold_40, HiC_scaffold_41, HiC_scaffold_42, HiC_scaffold_43, HiC_scaffold_44, HiC_scaffold_45, HiC_scaffold_46, HiC_scaffold_47, HiC_scaffold_48, HiC_scaffold_49, HiC_scaffold_50, HiC_scaffold_51, HiC_scaffold_52, HiC_scaffold_53, HiC_scaffold_54, HiC_scaffold_55, HiC_scaffold_56, HiC_scaffold_57, HiC_scaffold_58, HiC_scaffold_59, HiC_scaffold_60, HiC_scaffold_61, HiC_scaffold_62, HiC_scaffold_63, HiC_scaffold_64, HiC_scaffold_65, HiC_scaffold_66, HiC_scaffold_67, HiC_scaffold_68, HiC_scaffold_69, HiC_scaffold_70, HiC_scaffold_71, HiC_scaffold_72, HiC_scaffold_73, HiC_scaffold_74, HiC_scaffold_75, HiC_scaffold_76, HiC_scaffold_77, HiC_scaffold_78, HiC_scaffold_79, HiC_scaffold_80, HiC_scaffold_81, HiC_scaffold_82, HiC_scaffold_83, HiC_scaffold_84, HiC_scaffold_85, HiC_scaffold_86, HiC_scaffold_87, HiC_scaffold_88, HiC_scaffold_89, HiC_scaffold_90, HiC_scaffold_91, HiC_scaffold_92, HiC_scaffold_93, HiC_scaffold_94, HiC_scaffold_95, HiC_scaffold_96, HiC_scaffold_97, HiC_scaffold_98, HiC_scaffold_99, HiC_scaffold_100, HiC_scaffold_101, HiC_scaffold_102, HiC_scaffold_103, HiC_scaffold_104, HiC_scaffold_105, HiC_scaffold_106, HiC_scaffold_107, HiC_scaffold_108, HiC_scaffold_109, HiC_scaffold_110, HiC_scaffold_111, HiC_scaffold_112, HiC_scaffold_113, HiC_scaffold_114, HiC_scaffold_115, HiC_scaffold_116, HiC_scaffold_117, HiC_scaffold_118, HiC_scaffold_119, HiC_scaffold_120, HiC_scaffold_121, HiC_scaffold_122, HiC_scaffold_123, HiC_scaffold_124, HiC_scaffold_125, HiC_scaffold_126, HiC_scaffold_127, HiC_scaffold_128, HiC_scaffold_129, HiC_scaffold_130, HiC_scaffold_131, HiC_scaffold_132, HiC_scaffold_133, HiC_scaffold_134, HiC_scaffold_135, HiC_scaffold_136, HiC_scaffold_137, HiC_scaffold_138, HiC_scaffold_139, HiC_scaffold_140, HiC_scaffold_141, HiC_scaffold_142, HiC_scaffold_143, HiC_scaffold_144, HiC_scaffold_145, HiC_scaffold_146, HiC_scaffold_147, HiC_scaffold_148, HiC_scaffold_149, HiC_scaffold_150, HiC_scaffold_151, HiC_scaffold_152, HiC_scaffold_153, HiC_scaffold_154, HiC_scaffold_155, HiC_scaffold_156, HiC_scaffold_157, HiC_scaffold_158, HiC_scaffold_159, HiC_scaffold_160, HiC_scaffold_161, HiC_scaffold_162, HiC_scaffold_163, HiC_scaffold_164, HiC_scaffold_165, HiC_scaffold_166, HiC_scaffold_167, HiC_scaffold_168, HiC_scaffold_169, HiC_scaffold_170, HiC_scaffold_171, HiC_scaffold_172, HiC_scaffold_173, HiC_scaffold_174, HiC_scaffold_175, HiC_scaffold_176, HiC_scaffold_177, HiC_scaffold_178, HiC_scaffold_179, HiC_scaffold_180, HiC_scaffold_181, HiC_scaffold_182, HiC_scaffold_183, HiC_scaffold_184, HiC_scaffold_185, HiC_scaffold_186, HiC_scaffold_187, HiC_scaffold_188, HiC_scaffold_189, HiC_scaffold_190, HiC_scaffold_191, HiC_scaffold_192, HiC_scaffold_193, HiC_scaffold_194, HiC_scaffold_195, HiC_scaffold_196, HiC_scaffold_197, HiC_scaffold_198, HiC_scaffold_199, HiC_scaffold_200, HiC_scaffold_201, HiC_scaffold_202, HiC_scaffold_203, HiC_scaffold_204, HiC_scaffold_205, HiC_scaffold_206, HiC_scaffold_207, HiC_scaffold_208, HiC_scaffold_209, HiC_scaffold_210, HiC_scaffold_211, HiC_scaffold_212, HiC_scaffold_213, HiC_scaffold_214, HiC_scaffold_215, HiC_scaffold_216, HiC_scaffold_217, HiC_scaffold_218, HiC_scaffold_219, HiC_scaffold_220, HiC_scaffold_221, HiC_scaffold_222, HiC_scaffold_223, HiC_scaffold_224, HiC_scaffold_225, HiC_scaffold_226, HiC_scaffold_227, HiC_scaffold_228, HiC_scaffold_229, HiC_scaffold_230, HiC_scaffold_231, HiC_scaffold_232, HiC_scaffold_233, HiC_scaffold_234, HiC_scaffold_235, HiC_scaffold_236, HiC_scaffold_237, HiC_scaffold_238, HiC_scaffold_239, HiC_scaffold_240, HiC_scaffold_241, HiC_scaffold_242, HiC_scaffold_243, HiC_scaffold_244, HiC_scaffold_245, HiC_scaffold_246, HiC_scaffold_247, HiC_scaffold_248, HiC_scaffold_249, HiC_scaffold_250, HiC_scaffold_251, HiC_scaffold_252, HiC_scaffold_253, HiC_scaffold_254, HiC_scaffold_255, HiC_scaffold_256, HiC_scaffold_257, HiC_scaffold_258, HiC_scaffold_259, HiC_scaffold_260, HiC_scaffold_261, HiC_scaffold_262, HiC_scaffold_263, HiC_scaffold_264, HiC_scaffold_265, HiC_scaffold_266, HiC_scaffold_267, HiC_scaffold_268, HiC_scaffold_269, HiC_scaffold_270, HiC_scaffold_271, HiC_scaffold_272, HiC_scaffold_273, HiC_scaffold_274, HiC_scaffold_275, HiC_scaffold_276, HiC_scaffold_277, HiC_scaffold_278, HiC_scaffold_279, HiC_scaffold_280, HiC_scaffold_281, HiC_scaffold_282, HiC_scaffold_283, HiC_scaffold_284, HiC_scaffold_285, HiC_scaffold_286, HiC_scaffold_287, HiC_scaffold_288, HiC_scaffold_289, HiC_scaffold_290, HiC_scaffold_291, HiC_scaffold_292, HiC_scaffold_293, HiC_scaffold_294, HiC_scaffold_295, HiC_scaffold_296, HiC_scaffold_297, HiC_scaffold_298, HiC_scaffold_299, HiC_scaffold_300, HiC_scaffold_301, HiC_scaffold_302, HiC_scaffold_303, HiC_scaffold_304, HiC_scaffold_305, HiC_scaffold_306, HiC_scaffold_307, HiC_scaffold_308, HiC_scaffold_309, HiC_scaffold_310, HiC_scaffold_311, HiC_scaffold_312, HiC_scaffold_313, HiC_scaffold_314, HiC_scaffold_315, HiC_scaffold_316, HiC_scaffold_317, HiC_scaffold_318, HiC_scaffold_319, HiC_scaffold_320, HiC_scaffold_321, HiC_scaffold_322, HiC_scaffold_323, HiC_scaffold_324, HiC_scaffold_325, HiC_scaffold_326, HiC_scaffold_327, HiC_scaffold_328, HiC_scaffold_329, HiC_scaffold_330, HiC_scaffold_331, HiC_scaffold_332, HiC_scaffold_333, HiC_scaffold_334, HiC_scaffold_335, HiC_scaffold_336, HiC_scaffold_337, HiC_scaffold_338, HiC_scaffold_339, HiC_scaffold_340, HiC_scaffold_341, HiC_scaffold_342, HiC_scaffold_343, HiC_scaffold_344, HiC_scaffold_345, HiC_scaffold_346, HiC_scaffold_347, HiC_scaffold_348, HiC_scaffold_349, HiC_scaffold_350, HiC_scaffold_351, HiC_scaffold_352, HiC_scaffold_353, HiC_scaffold_354, HiC_scaffold_355, HiC_scaffold_356, HiC_scaffold_357, HiC_scaffold_358, HiC_scaffold_359, HiC_scaffold_360, HiC_scaffold_361, HiC_scaffold_362, HiC_scaffold_363, HiC_scaffold_364, HiC_scaffold_365, HiC_scaffold_366, HiC_scaffold_367, HiC_scaffold_368, HiC_scaffold_369, HiC_scaffold_370, HiC_scaffold_371, HiC_scaffold_372, HiC_scaffold_373, HiC_scaffold_374, HiC_scaffold_375, HiC_scaffold_376, HiC_scaffold_377, HiC_scaffold_378, HiC_scaffold_379, HiC_scaffold_380, HiC_scaffold_381, HiC_scaffold_382, HiC_scaffold_383, HiC_scaffold_384, HiC_scaffold_385, HiC_scaffold_386, HiC_scaffold_387, HiC_scaffold_388, HiC_scaffold_389, HiC_scaffold_390, HiC_scaffold_391, HiC_scaffold_392, HiC_scaffold_393, HiC_scaffold_394, HiC_scaffold_395, HiC_scaffold_396, HiC_scaffold_397, HiC_scaffold_398, HiC_scaffold_399, HiC_scaffold_400, HiC_scaffold_401, HiC_scaffold_402, HiC_scaffold_403, HiC_scaffold_404, HiC_scaffold_405, HiC_scaffold_406, HiC_scaffold_407, HiC_scaffold_408, HiC_scaffold_409, HiC_scaffold_410, HiC_scaffold_411, HiC_scaffold_412, HiC_scaffold_413, HiC_scaffold_414, HiC_scaffold_415, HiC_scaffold_416, HiC_scaffold_417, HiC_scaffold_418, HiC_scaffold_419, HiC_scaffold_420, HiC_scaffold_421, HiC_scaffold_422, HiC_scaffold_423, HiC_scaffold_424, HiC_scaffold_425, HiC_scaffold_426, HiC_scaffold_427, HiC_scaffold_428, HiC_scaffold_429, HiC_scaffold_430, HiC_scaffold_431, HiC_scaffold_432, HiC_scaffold_433, HiC_scaffold_434, HiC_scaffold_435, HiC_scaffold_436, HiC_scaffold_437, HiC_scaffold_438, HiC_scaffold_439, HiC_scaffold_440, HiC_scaffold_441, HiC_scaffold_442, HiC_scaffold_443, HiC_scaffold_444, HiC_scaffold_445, HiC_s"

#6. Calculate theotic value from the linear regressions and the WCE reads per Bin

    K4me3_0h_br1.theoretic.perBin = (0.96111 * WCE.K27ac_0h_br1.perBin) + 27.42451;
    K4me3_1h_br1.theoretic.perBin = (0.11971 * WCE.K27ac_1h_br1.perBin) + 6.64561;
    K4me3_4h_br1.theoretic.perBin = (0.44505 * WCE.K27ac_4h_br1.perBin) + 12.22014;

    K4me3_0h_br2.theoretic.perBin = (0.34377 * WCE.K27ac_0h_br2.perBin) + 13.10884;
    K4me3_1h_br2.theoretic.perBin = (0.25230 * WCE.K27ac_1h_br2.perBin) + 10.46680;
    K4me3_4h_br2.theoretic.perBin = (0.21612 * WCE.K27ac_4h_br2.perBin) + 3.01524;

#7. Calculate the residuals
    res_0h_br1 = K4me3_0h_br1.perBin - K4me3_0h_br1.theoretic.perBin;
    res_1h_br1 = K4me3_1h_br1.perBin - K4me3_1h_br1.theoretic.perBin;
    res_4h_br1 = K4me3_4h_br1.perBin - K4me3_4h_br1.theoretic.perBin;

    res_0h_br2 = K4me3_0h_br2.perBin - K4me3_0h_br2.theoretic.perBin;
    res_1h_br2 = K4me3_1h_br2.perBin - K4me3_1h_br2.theoretic.perBin;
    res_4h_br2 = K4me3_4h_br2.perBin - K4me3_4h_br2.theoretic.perBin;

#8. Replace all residuals < 0 with 0
    res_0h_br1[res_0h_br1 < 0] = 0;
    res_1h_br1[res_1h_br1 < 0] = 0;
    res_4h_br1[res_4h_br1 < 0] = 0;

    res_0h_br2[res_0h_br2 < 0] = 0;
    res_1h_br2[res_1h_br2 < 0] = 0;
    res_4h_br2[res_4h_br2 < 0] = 0;

#9. Keep only the entries were both replicates have reads
    badgenes_0h = which(rowSums(res_0h_br1)<1 | rowSums(res_0h_br2)<1 | rowSums(res_1h_br1)<1 | rowSums(res_1h_br2)<1 | rowSums(res_4h_br1)<1 | rowSums(res_4h_br2)<1);
    filtered_0h_br1 = res_0h_br1[-badgenes_0h,];
    filtered_0h_br2 = res_0h_br2[-badgenes_0h,];
    
    #1h
    filtered_1h_br1 = res_1h_br1[-badgenes_0h,];
    filtered_1h_br2 = res_1h_br2[-badgenes_0h,];

    #4h
    filtered_4h_br1 = res_4h_br1[-badgenes_0h,];
    filtered_4h_br2 = res_4h_br2[-badgenes_0h,];

length(filtered_0h_br1)

7720

#1. Average normalized replicates
    filtered_0h = ((res_0h_br1  /2530) + (res_0h_br2  /346))/2;
    filtered_1h = ((res_1h_br1  /3048) + (res_1h_br2  /1724))/2;
    filtered_4h = ((res_4h_br1  /4108) + (res_4h_br2  /1782))/2;

#9. Subsample residual matrices and plot metaplots
    res_0h.subs = metaSubsampleMatrix(filtered_0h);
    res_1h.subs = metaSubsampleMatrix(filtered_1h);
    res_4h.subs = metaSubsampleMatrix(filtered_4h);

#10. Give miningful names to each dataset --> thse names will be used as labels for the plot 
    res_0h.subs$sample.name = "0h ";
    res_1h.subs$sample.name = "1h ";
    res_4h.subs$sample.name = "4h ";

theme_set(
   theme_classic() +
        theme(
            panel.border = element_blank(),  
            # Remove panel background
            panel.background = element_blank(),
            legend.background = element_blank(),
            # Add axis line
            axis.line = element_line(colour = "black", size=0.5),
            panel.grid.major = element_line(colour = "white"),
            axis.text.x = element_text( color="black", size=14),
            axis.text.y = element_text( color="black", size=16),
            axis.title.x = element_text(color="black", size=14),
            axis.title.y = element_text(color="black", size=16)
            )
);

#11. The actual plotting
### V. Make mataplots to make sure the different normalization strategies produce the same metaprofiles ---> RPM norm data

# --> Enhancers

options(jupyter.plot_mimetypes="image/svg+xml", repr.plot.width=3, repr.plot.height=2);

plot.merged = rbind(res_0h.subs, res_1h.subs, res_4h.subs);

        ggplot(plot.merged, aes(x=x, y=mean, color=sample.name)) +
        geom_line(show.legend = F, lwd=0.7, alpha=0.8) +
        geom_ribbon( aes( ymin=lower, ymax=upper, fill=sample.name ), alpha=0.2, size=0, show.legend = F ) +
        #scale_colour_manual(values = c("#005ab3", "#ff8da1", "#ff6500")) +
        scale_colour_manual(values = c("#C10000", "#5900BA", "#ff9f1c")) +
        scale_y_continuous(labels = c(0, 2, 4), breaks=c(0.00, 0.02, 0.04)) +
        scale_x_continuous(labels = c(-2, -1, 0, 1, 2), breaks=c(0, 10, 20, 30, 40)) +
        labs(
            x = " Distance to TSS [kb]",
            y =  "Normalized \n signal "
        )

Scatterplot H3K4me1 vs H3

</center>

Promoters

#Import H3 Cut&Run Bam files:

##0h Trp
load("/home/danko_0001/projects/RawSequenceFiles/2019-11-06_K562_TrpATACseq_TrpCutRun/CutandRun_antiH3/align_hg19SacCer1/11283_11142_109460_HKLV3BGXC_CutRun_Cut_Run_0h_TAGCTT.Rdata");
CR0 = reads;
rm(reads);

##1h Trp
a = load("/home/danko_0001/projects/RawSequenceFiles/2019-11-06_K562_TrpATACseq_TrpCutRun/CutandRun_antiH3/align_hg19SacCer1/11283_11142_109460_HKLV3BGXC_CutRun_Cut_Run_1h_AGTTCC.Rdata");
CR1 = reads;
rm(reads);

##4h Trp
a = load("/home/danko_0001/projects/RawSequenceFiles/2019-11-06_K562_TrpATACseq_TrpCutRun/CutandRun_antiH3/align_hg19SacCer1/11283_11142_109460_HKLV3BGXC_CutRun_Cut_Run_4h_CCGTCC.Rdata");
CR4 = reads;
rm(reads);

#Subset each GRanges to nly have mono-nuc fragments
CR0_mono = CR0[width(CR0) >= 120 & width(CR0) < 180];
CR1_mono = CR1[width(CR1) >= 120 & width(CR1) < 180];
CR4_mono = CR4[width(CR4) >= 120 & width(CR4) < 180];

CR0_norm = CR0_mono;
CR1_norm = CR1_mono;
CR4_norm = CR4_mono;

#Correct the Cut&Run daa using spike-ins
#Multiply each BigWig by these normalization factors
CR0_norm$score = CR0_mono$count * 1;
CR1_norm$score = CR1_mono$count * 1.300083224;
CR4_norm$score = CR4_mono$count * 1.257619321;

#Overlap maxTSS with each mono-nucleosome Granges
    CR_p_0 = Count.reads.InBins(CR0_norm, promoters.maxTSS, spike = 1, binsize = 100, field = "score");
    CR_p_1 = Count.reads.InBins(CR1_norm, promoters.maxTSS, spike = 1, binsize = 100, field = "score");
    CR_p_4 = Count.reads.InBins(CR4_norm, promoters.maxTSS, spike = 1, binsize = 100, field = "score");

#Make matrix to run limma

scatter = tibble(
    K4me3_0h = (rowSums(res_0h_br1) + rowSums(res_0h_br2))/2,
    K4me3_1h = (rowSums(res_1h_br1) + rowSums(res_1h_br2))/2,
    K4me3_4h = (rowSums(res_4h_br1) + rowSums(res_4h_br2))/2,
    H3_0h    = rowSums(CR_p_0),
    H3_1h    = rowSums(CR_p_1),
    H3_4h    = rowSums(CR_p_4)


);

head(scatter)

A tibble: 6 × 6

K4me3_0h	K4me3_1h	K4me3_4h	H3_0h	H3_1h	H3_4h
<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
1432.85370	419.49468	857.29656	10	12	5
49.59815	12.34270	85.60742	17	7	2
1014.51597	250.17208	602.80796	11	3	2
937.35234	342.03511	589.53700	13	8	4
706.23136	212.06016	480.43168	6	8	5
93.13324	19.15575	135.67336	3	8	1

scatter.filt = scatter[scatter$K4me3_0h > 1, ];
scatter.filt = scatter.filt[scatter.filt$K4me3_1h > 1, ];
scatter.filt = scatter.filt[scatter.filt$K4me3_4h > 1, ];

cor.test(scatter.filt$K4me3_0h, scatter.filt$H3_0h, method="spearman");
cor.test(scatter.filt$K4me3_0h, scatter.filt$H3_0h, method="pearson");

	Spearman's rank correlation rho

data:  scatter.filt$K4me3_0h and scatter.filt$H3_0h
S = 1.4108e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.2374296 

	Pearson's product-moment correlation

data:  scatter.filt$K4me3_0h and scatter.filt$H3_0h
t = 38.242, df = 10352, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.3348367 0.3685937
sample estimates:
      cor 
0.3518296 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_0h, H3_0h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n H3K4me3 versus H3 \n S = 0.2374296, P = 0.3518296 \n",
        x = "H3K4me3 0h",
        y = "H3 0h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

cor.test(scatter.filt$K4me3_1h, scatter.filt$H3_1h, method="spearman");
cor.test(scatter.filt$K4me3_1h, scatter.filt$H3_1h, method="pearson");

	Spearman's rank correlation rho

data:  scatter.filt$K4me3_1h and scatter.filt$H3_1h
S = 1.3572e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.2663835 

	Pearson's product-moment correlation

data:  scatter.filt$K4me3_1h and scatter.filt$H3_1h
t = 39.458, df = 10352, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.3447102 0.3781996
sample estimates:
      cor 
0.3615715 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_1h, H3_1h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n H3K4me3 versus H3 \n S = 0.2663835, P = 0.3615715 \n",
        x = "H3K4me3 1h",
        y = "H3 1h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

cor.test(scatter.filt$K4me3_4h, scatter.filt$H3_4h, method="spearman");
cor.test(scatter.filt$K4me3_4h, scatter.filt$H3_4h, method="pearson");

	Spearman's rank correlation rho

data:  scatter.filt$K4me3_4h and scatter.filt$H3_4h
S = 1.3452e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
    rho 
0.27287 

	Pearson's product-moment correlation

data:  scatter.filt$K4me3_4h and scatter.filt$H3_4h
t = 35.502, df = 10352, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.3121743 0.3465185
sample estimates:
      cor 
0.3294554 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_4h, H3_4h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    #scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n H3K4me3 versus H3 \n S = 0.27287, P = 0.3294554 \n",
        x = "H3K4me3 4h",
        y = "H3 4h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

Log2FC

# Compute log2FC
    K4me3.log2FC = log2(scatter.filt$K4me3_4h / scatter.filt$K4me3_0h);
    H3.log2FC    = log2(scatter.filt$H3_4h    / scatter.filt$H3_0h);

# Merge 
    K4me3_H3_log2FC = cbind(K4me3.log2FC, H3.log2FC);
    colnames(K4me3_H3_log2FC) = c("K4me3_04", "H3_04");
    K4me3_H3_log2FC = as.data.frame(K4me3_H3_log2FC);

# Remove TSS with infinite values
    K4me3_H3_log2FC = K4me3_H3_log2FC[is.finite(rowSums(K4me3_H3_log2FC)),];
#9665

K4me3_H3_log2FC[K4me3_H3_log2FC$K4me3_04 < 0, ]

A data.frame: 5262 × 2

	K4me3_04	H3_04
	<dbl>	<dbl>
1	-0.741025053	-1.0000000
3	-0.751021196	-2.4594316
4	-0.669009086	-1.7004397
5	-0.555809598	-0.2630344
7	-0.395517186	-0.3219281
8	-0.756926005	-1.5849625
9	-0.411062579	-1.7004397
11	-0.871135078	0.0000000
13	-0.470624297	-0.7369656
14	-0.301230654	-2.0000000
15	-0.402705062	-0.1926451
16	-0.780737230	-0.7776076
17	-0.715910704	-1.7004397
19	-0.494697097	-0.8073549
21	-0.346029041	0.2223924
22	-0.162221096	-1.5849625
24	-0.769150443	0.1375035
25	-0.205658073	-1.5849625
26	-0.370000967	-1.0995357
28	-0.289582560	-1.0000000
29	-0.013566602	-0.3625701
30	-0.444844892	0.0000000
31	-0.769813609	-0.1375035
32	-0.258388130	-0.8930848
33	-0.513039769	-1.8073549
35	-0.542113550	-1.5849625
38	-0.005449026	-2.0000000
40	-0.349569965	-1.5025003
42	-0.401339532	0.8930848
43	-0.177187356	-1.0000000
⋮	⋮	⋮
10229	-0.82938601	-1.8744691
10230	-0.09212628	0.5849625
10231	-0.55135746	-0.8744691
10232	-0.47920494	-2.0000000
10235	-0.46219911	1.0780025
10236	-0.85984331	0.5849625
10248	-0.47706927	-0.8479969
10255	-0.35782993	0.4854268
10259	-0.20352585	-2.1699250
10271	-0.21971021	0.5849625
10273	-0.20820714	-1.3219281
10274	-0.03795069	-2.4594316
10280	-0.70293520	-1.7369656
10287	-0.26645931	-1.7369656
10291	-0.10390801	-0.8479969
10294	-0.23326875	0.5849625
10303	-0.09632808	-0.5849625
10313	-0.57879898	-0.2223924
10315	-0.13093482	-2.0000000
10316	-0.18300941	-1.5849625
10317	-1.07910737	-1.2630344
10318	-0.37029795	-0.7369656
10319	-0.58640658	-1.4150375
10325	-0.18997347	1.4150375
10329	-0.81454761	-0.8073549
10330	-0.33945775	-2.5849625
10337	-0.43178048	2.0000000
10338	-0.34762096	-0.4854268
10340	-0.36501301	-2.3219281
10345	-0.49992393	0.0000000

cor.test(K4me3_H3_log2FC$K4me3_04, K4me3_H3_log2FC$H3_04, method="spearman");
cor.test(K4me3_H3_log2FC$K4me3_04, K4me3_H3_log2FC$H3_04, method="pearson");

	Spearman's rank correlation rho

data:  K4me3_H3_log2FC$K4me3_04 and K4me3_H3_log2FC$H3_04
S = 1.7271e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
       rho 
-0.1477697 

	Pearson's product-moment correlation

data:  K4me3_H3_log2FC$K4me3_04 and K4me3_H3_log2FC$H3_04
t = -12.515, df = 9663, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 -0.1458644 -0.1066264
sample estimates:
       cor 
-0.1262948 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(K4me3_H3_log2FC), mapping=aes(K4me3_04, H3_04)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4, slope = -1) +
    #scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n H3K4me3 versus H3 \n S = -0.1477697, P = -0.1262948 \n",
        x = "H3K4me3 4h/0h",
        y = "H3 4h/0h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

# Compute log2FC
    K4me3.log2FC_01 = log2(scatter.filt$K4me3_1h / scatter.filt$K4me3_0h);
    H3.log2FC_01    = log2(scatter.filt$H3_1h    / scatter.filt$H3_0h);

# Merge 
    K4me3_H3_log2FC_01 = cbind(K4me3.log2FC_01, H3.log2FC_01);
    colnames(K4me3_H3_log2FC_01) = c("K4me3_01", "H3_01");
    K4me3_H3_log2FC_01 = as.data.frame(K4me3_H3_log2FC_01);

# Remove TSS with infinite values
    K4me3_H3_log2FC_01 = K4me3_H3_log2FC_01[is.finite(rowSums(K4me3_H3_log2FC_01)),];

cor.test(K4me3_H3_log2FC_01$K4me3_01, K4me3_H3_log2FC_01$H3_01, method="spearman");
cor.test(K4me3_H3_log2FC_01$K4me3_01, K4me3_H3_log2FC_01$H3_01, method="pearson");

	Spearman's rank correlation rho

data:  K4me3_H3_log2FC_01$K4me3_01 and K4me3_H3_log2FC_01$H3_01
S = 1.8168e+11, p-value = 1.794e-06
alternative hypothesis: true rho is not equal to 0
sample estimates:
        rho 
-0.04741578 

	Pearson's product-moment correlation

data:  K4me3_H3_log2FC_01$K4me3_01 and K4me3_H3_log2FC_01$H3_01
t = -5.8132, df = 10132, p-value = 6.313e-09
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 -0.07703986 -0.03822916
sample estimates:
        cor 
-0.05765629 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(K4me3_H3_log2FC), mapping=aes(K4me3_04, H3_04)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4, slope = -1) +
    #scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n H3K4me3 versus H3 \n S = -0.04741578, P = -0.05765629 \n",
        x = "H3K4me3 1h/0h",
        y = "H3 1h/0h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

Correlate H3K4me3 signal with either pause or GB PROseq signal

</center>

#Import PROseq BigWigs
    PROseq_0h_plus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_0h_plus_normalized_NateWay.bw");
    PROseq_1h_plus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_1h_plus_normalized_NateWay.bw");
    PROseq_4h_plus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_4h_plus_normalized_NateWay.bw");

    PROseq_0h_minus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_0h_minus_normalized_NateWay.bw");
    PROseq_1h_minus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_1h_minus_normalized_NateWay.bw");
    PROseq_4h_minus = import.bw("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/merged_ChROseq/BigWig_outputs/ChROseq_merged_4h_minus_normalized_NateWay.bw");

#Set strand manually    
    strand(PROseq_0h_plus) = "+";
    strand(PROseq_1h_plus) = "+";
    strand(PROseq_4h_plus) = "+";

    strand(PROseq_0h_minus) = "-";
    strand(PROseq_1h_minus) = "-";
    strand(PROseq_4h_minus) = "-";

#Merge PROseq per time point
    PROseq_0h = append(PROseq_0h_plus, PROseq_0h_minus);
    PROseq_1h = append(PROseq_1h_plus, PROseq_1h_minus);
    PROseq_4h = append(PROseq_4h_plus, PROseq_4h_minus);

#Normalize PROseq data by dividing with the total number of spike-in reads in each sample:
#   --> score = not normalized reads
#   --> count = normalized reads

    PROseq_0h$count = PROseq_0h$score * 1/1;
    PROseq_1h$count = PROseq_1h$score * 1/1;
    PROseq_4h$count = PROseq_4h$score * 1/1;

#1. Import gene coordinates in hg19
    genes=read.table("/local/storage/projects/RawSequenceFiles/2019-07-06_K562_ChIP_TriptolideTimecourse/merged_datasets_JuneJuly2019/masked_Diulia/gencode.v19.annotation.gtf.gz", header=F, stringsAsFactors=F);
    colnames(genes) = c("chr", "Transcript", "start", "end", "strand", "gene_id", "transcript_id", "gene_type", "gene_name", "TranscriptName");
    genes = genes[genes$Transcript =="transcript",];
    genes = as(genes, "GRanges");

    #Order genes based on their length
    genes = genes[order(width(genes))];
    genes = genes[!duplicated(genes$gene_name)];
    genes = genes[width(genes) > 250];

    #genes_resize = promoters(genes, upstream=2000, downstream=2000);

#Get separate coordinates for pause site and GB
    #GB
    promoters.GB.coord  = genebodies(genes, start = 200, end = -200, fix.start = "start", fix.end = "end");

    #Start-to-pause coordinates
    promoters.Pause.coord  = genebodies(genes, start = 0, end = 200, fix.start = "start", fix.end = "start");

#Compute coverage of the Rdata provided as hist.mark
        PROseq_0h = makeGRangesBRG(PROseq_0h);
        PROseq_1h = makeGRangesBRG(PROseq_1h);
        PROseq_4h = makeGRangesBRG(PROseq_4h);


#Count hist.mark signal per GB
    PROseq.0h_GB = getCountsByRegions(PROseq_0h, promoters.GB.coord, field = "count");
    PROseq.1h_GB = getCountsByRegions(PROseq_1h, promoters.GB.coord, field = "count");
    PROseq.4h_GB = getCountsByRegions(PROseq_4h, promoters.GB.coord, field = "count");

#Count hist.mark signal per Pause
    PROseq.0h_Pause = getCountsByRegions(PROseq_0h, promoters.Pause.coord, field = "count");
    PROseq.1h_Pause = getCountsByRegions(PROseq_1h, promoters.Pause.coord, field = "count");
    PROseq.4h_Pause = getCountsByRegions(PROseq_4h, promoters.Pause.coord, field = "count");

#Get H3K4me3 signal per gene and average normalized replicates
    filtered_0h = ((res_0h_br1  /2530) + (res_0h_br2  /346))/2;
    filtered_1h = ((res_1h_br1  /3048) + (res_1h_br2  /1724))/2;
    filtered_4h = ((res_4h_br1  /4108) + (res_4h_br2  /1782))/2;

write.table(rowSums(filtered_0h), "./H3K4me3.0h_SignalPerGeneLarger250bp.bed", quote=F, sep="\t", row.names=F, col.names=F);
write.table(rowSums(filtered_4h), "./H3K4me3.4h_SignalPerGeneLarger250bp.bed", quote=F, sep="\t", row.names=F, col.names=F);

#Make matrix to run limma

scatter = tibble(
    PROseq.GB_0h = abs(PROseq.0h_GB),
    PROseq.GB_1h = abs(PROseq.1h_GB),
    PROseq.GB_4h = abs(PROseq.4h_GB),
    
    PROseq.Pause_0h = abs(PROseq.0h_Pause),
    PROseq.Pause_1h = abs(PROseq.1h_Pause),
    PROseq.Pause_4h = abs(PROseq.4h_Pause),

    K4me3_0h    = rowSums(filtered_0h),
    K4me3_1h    = rowSums(filtered_1h),
    K4me3_4h    = rowSums(filtered_4h)


);

head(scatter)

A tibble: 6 × 9

PROseq.GB_0h	PROseq.GB_1h	PROseq.GB_4h	PROseq.Pause_0h	PROseq.Pause_1h	PROseq.Pause_4h	K4me3_0h	K4me3_1h	K4me3_4h
<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
0	0.000000	0	0	0.000000	0.000000	0.0000000	0.00000000	0.00000000
0	0.000000	0	0	0.000000	0.000000	0.0000000	0.00000000	0.00000000
0	2.787623	0	5	4.181434	4.085787	0.1870537	0.01757447	0.05522856
0	0.000000	0	0	0.000000	0.000000	0.0000000	0.00000000	0.00000000
0	0.000000	0	0	0.000000	0.000000	0.0000000	0.00000000	0.00000000
0	0.000000	0	0	0.000000	0.000000	0.0000000	0.00000000	0.00000000

scatter.filt = scatter[scatter$PROseq.GB_0h > 0, ];
scatter.filt = scatter.filt[scatter.filt$PROseq.GB_1h > 0, ];
scatter.filt = scatter.filt[scatter.filt$PROseq.GB_4h > 0, ];

cor.test(scatter.filt$K4me3_0h, scatter.filt$PROseq.GB_0h, method="spearman");
cor.test(scatter.filt$K4me3_0h, scatter.filt$PROseq.GB_0h, method="pearson");

	Spearman's rank correlation rho

data:  scatter.filt$K4me3_0h and scatter.filt$PROseq.GB_0h
S = 3.7282e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.5536334 

	Pearson's product-moment correlation

data:  scatter.filt$K4me3_0h and scatter.filt$PROseq.GB_0h
t = 34.144, df = 7941, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.3384605 0.3768166
sample estimates:
      cor 
0.3577895 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(PROseq.GB_0h, K4me3_0h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    #geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.5479982, P = 0.3887045 \n",
        y = "H3K4me3 0h",
        x = "PROseq - GeneBody 0h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_1h, PROseq.GB_1h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.421042, P = 0.2597497 \n",
        x = "H3K4me3 1h",
        y = "PROseq - GeneBody 1h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(K4me3_4h, PROseq.GB_4h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.1946126, P = 0.08440513 \n",
        x = "H3K4me3 4h",
        y = "PROseq - GeneBody 4h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

cor.test(scatter.filt$K4me3_0h, scatter.filt$PROseq.Pause_0h, method="spearman");
cor.test(scatter.filt$K4me3_0h, scatter.filt$PROseq.Pause_0h, method="pearson");

	Spearman's rank correlation rho

data:  scatter.filt$K4me3_0h and scatter.filt$PROseq.Pause_0h
S = 2.5431e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.6955184 

	Pearson's product-moment correlation

data:  scatter.filt$K4me3_0h and scatter.filt$PROseq.Pause_0h
t = 47.191, df = 7941, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.4506386 0.4849932
sample estimates:
      cor 
0.4679927 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(PROseq.Pause_0h, K4me3_0h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    #geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.6901721, P = 0.4765192 \n",
        y = "H3K4me3 0h",
        x = "PROseq - Pause 0h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(PROseq.Pause_1h, K4me3_1h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.5891095, P = 0.5099145 \n",
        y = "H3K4me3 1h",
        x = "PROseq - Pause 1h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.filt), mapping=aes(PROseq.Pause_4h, K4me3_4h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.3589597, P = 0.2611949 \n",
        y = "H3K4me3 4h",
        x = "PROseq - Pause 4h"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

Compare log2FC 04

</center>

#Make matrix to run limma

scatter.log2FC = tibble(
    PROseq.GB_04h = log2(abs(PROseq.4h_GB)/(abs(PROseq.0h_GB)+1)),
    PROseq.Pause_04h = log2(abs(PROseq.4h_Pause)/(abs(PROseq.0h_Pause)+1)),
    K4me3_04h    = log2((rowSums(filtered_4h))/(rowSums(filtered_0h)+1))  


);


scatter.log2FC =  scatter.log2FC[is.finite(rowSums(scatter.log2FC)),];
#scatter.log2FC =  scatter.log2FC[scatter.log2FC$K4me3_04h > -5, ];

cor.test(scatter.log2FC$K4me3_04h, scatter.log2FC$PROseq.GB_04h, method="spearman");
cor.test(scatter.log2FC$K4me3_04h, scatter.log2FC$PROseq.GB_04h, method="pearson");

	Spearman's rank correlation rho

data:  scatter.log2FC$K4me3_04h and scatter.log2FC$PROseq.GB_04h
S = 852409639, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
       rho 
-0.4140822 

	Pearson's product-moment correlation

data:  scatter.log2FC$K4me3_04h and scatter.log2FC$PROseq.GB_04h
t = -22.913, df = 1533, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 -0.5414324 -0.4668465
sample estimates:
       cor 
-0.5050819 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.log2FC), mapping=aes(PROseq.GB_04h, K4me3_04h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    #geom_abline(alpha=0.4) +
    #scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.3302053, P = 0.4100412 \n",
        y = "H3K4me3 log2(0h/4h)",
        x = "PROseq - GebeBody log2(0h/4h)"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

cor.test(scatter.log2FC$K4me3_04h, scatter.log2FC$PROseq.Pause_04h, method="spearman");
cor.test(scatter.log2FC$K4me3_04h, scatter.log2FC$PROseq.Pause_04h, method="pearson");

	Spearman's rank correlation rho

data:  scatter.log2FC$K4me3_04h and scatter.log2FC$PROseq.Pause_04h
S = 669210733, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
       rho 
-0.3876175 

	Pearson's product-moment correlation

data:  scatter.log2FC$K4me3_04h and scatter.log2FC$PROseq.Pause_04h
t = -19.296, df = 1423, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 -0.4956075 -0.4132428
sample estimates:
       cor 
-0.4553991 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.log2FC), mapping=aes(PROseq.Pause_04h, K4me3_04h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    #geom_abline(alpha=0.4) +
    #scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.4255293, P = 0.6121219 \n",
        y = "H3K4me3 log2(0h/4h)",
        x = "PROseq - Pause log2(0h/4h)"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

Compare H3K4me3 with Pause index

</center>

*Pause Index = Pause.signal/GB.signal

#Make matrix to run limma

scatter.PauseIndex = tibble(
    PROseq.0h_PI = abs(PROseq.0h_Pause)/(abs(PROseq.0h_GB)),
    PROseq.1h_PI = abs(PROseq.1h_Pause)/(abs(PROseq.1h_GB)),
    PROseq.4h_PI = abs(PROseq.4h_Pause)/(abs(PROseq.4h_GB)),

    K4me3.0h_PI    = rowSums(filtered_0h),
    K4me3.1h_PI    = rowSums(filtered_1h),
    K4me3.4h_PI    = rowSums(filtered_4h)

);


scatter.PauseIndex =  scatter.PauseIndex[is.finite(rowSums(scatter.PauseIndex)),];

cor.test(scatter.PauseIndex$K4me3.0h_PI, scatter.PauseIndex$PROseq.0h_PI, method="spearman");
cor.test(scatter.PauseIndex$K4me3.0h_PI, scatter.PauseIndex$PROseq.0h_PI, method="pearson");

	Spearman's rank correlation rho

data:  scatter.PauseIndex$K4me3.0h_PI and scatter.PauseIndex$PROseq.0h_PI
S = 4.1583e+10, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.5021315 

	Pearson's product-moment correlation

data:  scatter.PauseIndex$K4me3.0h_PI and scatter.PauseIndex$PROseq.0h_PI
t = 16.403, df = 7941, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.1596727 0.2022163
sample estimates:
      cor 
0.1810292 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.PauseIndex), mapping=aes(PROseq.0h_PI, K4me3.0h_PI)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    geom_abline(alpha=0.4) +
    scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.4968961, P = 0.1933199 \n",
        y = "H3K4me3 0h",
        x = "PROseq 0h - PauseIndex"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )

cor.test(scatter.PauseIndex$K4me3.1h_PI, scatter.PauseIndex$PROseq.1h_PI, method="spearman");
cor.test(scatter.PauseIndex$K4me3.1h_PI, scatter.PauseIndex$PROseq.1h_PI, method="pearson");

	Spearman's rank correlation rho

data:  scatter.PauseIndex$K4me3.1h_PI and scatter.PauseIndex$PROseq.1h_PI
S = 6.523e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.4670988 

	Pearson's product-moment correlation

data:  scatter.PauseIndex$K4me3.1h_PI and scatter.PauseIndex$PROseq.1h_PI
t = 21.484, df = 19436, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.1385459 0.1660101
sample estimates:
      cor 
0.1523074 

cor.test(scatter.PauseIndex$K4me3.4h_PI, scatter.PauseIndex$PROseq.4h_PI, method="spearman");
cor.test(scatter.PauseIndex$K4me3.4h_PI, scatter.PauseIndex$PROseq.4h_PI, method="pearson");

	Spearman's rank correlation rho

data:  scatter.PauseIndex$K4me3.4h_PI and scatter.PauseIndex$PROseq.4h_PI
S = 8.6453e+11, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.2937223 

	Pearson's product-moment correlation

data:  scatter.PauseIndex$K4me3.4h_PI and scatter.PauseIndex$PROseq.4h_PI
t = 9.2811, df = 19436, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.05241662 0.08040883
sample estimates:
      cor 
0.0664258 

Compare log2FC 04 - PauseIndex

</center>

*Pause Index = Pause.signal/GB.signal

#Make matrix to run limma

scatter.log2FC.PI = tibble(
    PROseq.04h_PI = log2( abs(PROseq.4h_Pause)/abs(PROseq.4h_GB) / (abs(PROseq.0h_Pause)/(abs(PROseq.0h_GB))) ),
    K4me3_04h     = log2( ((rowSums(filtered_4h)+1) ) / (rowSums(filtered_0h)+1) )  


);


scatter.log2FC.PI =  scatter.log2FC.PI[is.finite(rowSums(scatter.log2FC.PI)),];
#scatter.log2FC.PI =  scatter.log2FC.PI[scatter.log2FC.PI$K4me3_04h < 0, ];

cor.test(scatter.log2FC.PI$K4me3_04h, scatter.log2FC.PI$PROseq.04h_PI, method="spearman");
cor.test(scatter.log2FC.PI$K4me3_04h, scatter.log2FC.PI$PROseq.04h_PI, method="pearson");

	Spearman's rank correlation rho

data:  scatter.log2FC.PI$K4me3_04h and scatter.log2FC.PI$PROseq.04h_PI
S = 1134619808, p-value < 2.2e-16
alternative hypothesis: true rho is not equal to 0
sample estimates:
      rho 
0.3282156 

	Pearson's product-moment correlation

data:  scatter.log2FC.PI$K4me3_04h and scatter.log2FC.PI$PROseq.04h_PI
t = 14.26, df = 2162, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.2542082 0.3312490
sample estimates:
      cor 
0.2932045 

options(warn=-1)


options(jupyter.plot_mimetypes="image/png", repr.plot.width=7, repr.plot.height=6);

ggplot(as.data.frame(scatter.log2FC.PI), mapping=aes(PROseq.04h_PI, K4me3_04h)) + geom_point() +
    #The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument,
    #where adjust = 0.5 means use half of the default bandwidth.
    geom_pointdensity(adjust = 10, size = 2) +
    scale_color_viridis()+
    #geom_abline(alpha=0.4) +
    #scale_x_log10() + scale_y_log10() +
    labs(
        title = "\n  S = 0.3282156, P = 0.2932045 \n",
        y = "H3K4me3 log2(4h/0h)",
        x = "PROseq - PauseIndex log2(4h/0h)"
    ) +
    theme_classic() +
    theme(
        #panel.border = element_blank(),  
        # Remove panel background
        panel.background = element_blank(),
        legend.background = element_blank(),
        # Add axis line
        axis.line = element_line(colour = "black", size=1),
        panel.grid.major = element_line(colour = "white"),
        plot.title = element_text(color="black", size=24, face="bold", hjust = 0.5),
        axis.text.x = element_text( color="black", size=20, margin=margin(t = 1, r = 0, b = 2, l = 0)),
        axis.text.y = element_text( color="black", size=20, margin=margin(t = 0, r = 1, b = 0, l = 5)),
        axis.title.x = element_text(color="black", size=28, face="bold", margin = margin(t = 20, r = 0, b = 1, l = 0)),
        axis.title.y = element_text(color="black", size=24, face="bold", margin = margin(t = 0, r = 2, b = 0, l = 10))
    )